Exploration
Seraphina Shi
Load Data from the Clock Calculator
Table with summarize info [table 1]
For all observations (including the control group)
| Characteristic | N = 1411 |
|---|---|
| Group | |
| LCW Clean Ctrl | 12 / 141 (8.5%) |
| LEX | 129 / 141 (91%) |
| Gender | |
| F | 140 / 141 (99%) |
| U | 1 / 141 (0.7%) |
| DNAmAge | 57 (14) |
| DNAmAgeHannum | 60 (14) |
| DNAmPhenoAge | 56 (13) |
| DNAmAgeSkinBloodClock | 56 (13) |
| DNAmGrimAge | 56 (11) |
| DNAmTL | 6.80 (0.33) |
| AgeAccelerationResidual | -0.1 (5.1) |
| AgeAccelerationResidualHannum | -0.1 (4.9) |
| AgeAccelPheno | -0.1 (5.1) |
| DNAmAgeSkinBloodClockAdjAge | 0.0 (3.7) |
| AgeAccelGrim | -0.1 (3.4) |
| DNAmTLAdjAge | 0.00 (0.24) |
| IEAA | 0.0 (4.5) |
| EEAA | -0.1 (6.0) |
| Age | 57 (14) |
| county | |
| Fuyuan | 61 / 119 (51%) |
| Xuanwe | 58 / 119 (49%) |
| (Missing) | 22 |
| BMI | 22.0 (3.5) |
| (Missing) | 12 |
| ses | 54 / 119 (45%) |
| (Missing) | 22 |
| edu | |
| 1 | 81 / 119 (68%) |
| 2 | 19 / 119 (16%) |
| 3 | 14 / 119 (12%) |
| 4 | 5 / 119 (4.2%) |
| (Missing) | 22 |
| curFuel | |
| Gas/Elect | 12 / 124 (9.7%) |
| Smokeles | 17 / 124 (14%) |
| Smoky | 87 / 124 (70%) |
| Wood_and_or_Plant | 8 / 124 (6.5%) |
| (Missing) | 17 |
| brthFuel | |
| Gas/Elect | 12 / 128 (9.4%) |
| Mix | 53 / 128 (41%) |
| Smokeles | 5 / 128 (3.9%) |
| Smoky | 47 / 128 (37%) |
| Wood | 11 / 128 (8.6%) |
| (Missing) | 13 |
| cumFuel | |
| Gas/Elect | 12 / 131 (9.2%) |
| Mix | 82 / 131 (63%) |
| Smoky | 37 / 131 (28%) |
| (Missing) | 10 |
| curStove | |
| Firepit_and_unventilated | 22 / 124 (18%) |
| Gas/Elect | 12 / 124 (9.7%) |
| Mix | 19 / 124 (15%) |
| Portable_stove | 20 / 124 (16%) |
| Ventilated | 51 / 124 (41%) |
| (Missing) | 17 |
| bap_air | 65 (87) |
| (Missing) | 17 |
| pm25_air | 197 (176) |
| (Missing) | 12 |
| ANY_air | 1,038 (1,792) |
| (Missing) | 53 |
| BPE_air | 71 (92) |
| (Missing) | 17 |
| BaA_air | 88 (145) |
| (Missing) | 17 |
| BbF_air | 106 (143) |
| (Missing) | 17 |
| BkF_air | 23 (32) |
| (Missing) | 17 |
| CHR_air | 83 (133) |
| (Missing) | 17 |
| DBA_air | 24 (36) |
| (Missing) | 17 |
| FLT_air | 60 (136) |
| (Missing) | 17 |
| FLU_air | 486 (680) |
| (Missing) | 53 |
| IPY_air | 43 (51) |
| (Missing) | 17 |
| NAP_air | 5,731 (8,737) |
| (Missing) | 53 |
| PHE_air | 730 (1,054) |
| (Missing) | 53 |
| PYR_air | 66 (139) |
| (Missing) | 17 |
| Benzanthracene_Chrysene_urine | 0.92 (3.17) |
| (Missing) | 14 |
| Naphthalene_urine | 224 (686) |
| (Missing) | 12 |
| Methylnaphthalene_2_urine | 46 (59) |
| (Missing) | 21 |
| Methylnaphthalene_1_urine | 20 (24) |
| (Missing) | 16 |
| Acenaphthene_urine | 7 (11) |
| (Missing) | 12 |
| Phenanthrene_Anthracene_urine | 204 (275) |
| (Missing) | 12 |
| Fluoranthene_urine | 21 (23) |
| (Missing) | 12 |
| Pyrene_urine | 0.71 (0.57) |
| (Missing) | 30 |
| CUR6_BC_PAH6 | 0.21 (0.98) |
| (Missing) | 25 |
| CUR6_PAH31 | 0.20 (0.92) |
| (Missing) | 25 |
| CUR6_NkF | -0.11 (1.10) |
| (Missing) | 25 |
| CUR6_PM_RET | -0.01 (0.93) |
| (Missing) | 25 |
| CUR6_NO2 | 0.19 (0.99) |
| (Missing) | 25 |
| CUR6_SO2 | -0.13 (0.89) |
| (Missing) | 25 |
| CHLD5_X7 | -0.02 (0.92) |
| (Missing) | 25 |
| CHLD5_X33 | 0.18 (0.98) |
| (Missing) | 25 |
| CHLD5_NkF | -0.11 (1.13) |
| (Missing) | 25 |
| CHLD5_NO2 | 0.23 (1.09) |
| (Missing) | 25 |
| CHLD5_SO2 | 0.02 (0.88) |
| (Missing) | 25 |
| CUM6_BC_NO2_PM | 0.11 (1.01) |
| (Missing) | 25 |
| CUM6_PAH36 | 0.21 (0.97) |
| (Missing) | 25 |
| CUM6_DlP | -0.20 (1.04) |
| (Missing) | 25 |
| CUM6_NkF | -0.04 (1.11) |
| (Missing) | 25 |
| CUM6_RET | -0.09 (0.97) |
| (Missing) | 25 |
| CUM6_SO2 | -0.07 (0.93) |
| (Missing) | 25 |
| MEAS6_BC_PM_RET | 0.04 (0.93) |
| (Missing) | 97 |
| MEAS6_X31 | 0.06 (1.05) |
| (Missing) | 97 |
| MEAS6_X5 | 0.01 (1.00) |
| (Missing) | 97 |
| MEAS6_DlP | 0.02 (1.00) |
| (Missing) | 97 |
| MEAS6_NkF | 0.08 (1.04) |
| (Missing) | 97 |
| MEAS6_NO2_SO2 | -0.03 (0.99) |
| (Missing) | 97 |
| URI5_NAP_1M_2M | 0.01 (0.96) |
| (Missing) | 37 |
| URI5_ACE | -0.06 (0.99) |
| (Missing) | 37 |
| URI5_FLU_PHE | -0.05 (0.95) |
| (Missing) | 37 |
| URI5_PYR | -0.02 (0.91) |
| (Missing) | 37 |
| URI5_CHR | -0.01 (1.01) |
| (Missing) | 37 |
|
1
n / N (%); Mean (SD)
|
|
For observations in the treatment group
| Characteristic | N = 1291 |
|---|---|
| SbjctD | 297 (129) |
| (Missing) | 10 |
| Visit | |
| 1 | 91 / 119 (76%) |
| 2 | 28 / 119 (24%) |
| (Missing) | 10 |
| Group | |
| LEX | 129 / 129 (100%) |
| Gender | |
| F | 128 / 129 (99%) |
| U | 1 / 129 (0.8%) |
| DNAmAge | 58 (13) |
| DNAmAgeHannum | 60 (14) |
| DNAmPhenoAge | 56 (14) |
| DNAmAgeSkinBloodClock | 57 (13) |
| DNAmGrimAge | 56 (11) |
| DNAmTL | 6.82 (0.32) |
| AgeAccelerationResidual | 0.4 (4.7) |
| AgeAccelerationResidualHannum | -0.2 (4.0) |
| AgeAccelPheno | -0.3 (4.3) |
| DNAmAgeSkinBloodClockAdjAge | 0.2 (3.4) |
| AgeAccelGrim | -0.43 (2.99) |
| DNAmTLAdjAge | 0.03 (0.18) |
| IEAA | 0.2 (4.3) |
| EEAA | -0.3 (5.1) |
| Age | 58 (15) |
| county | |
| Fuyuan | 61 / 119 (51%) |
| Xuanwe | 58 / 119 (49%) |
| (Missing) | 10 |
| BMI | 22.0 (3.5) |
| ses | 54 / 119 (45%) |
| (Missing) | 10 |
| edu | |
| 1 | 81 / 119 (68%) |
| 2 | 19 / 119 (16%) |
| 3 | 14 / 119 (12%) |
| 4 | 5 / 119 (4.2%) |
| (Missing) | 10 |
| curFuel | |
| Smokeles | 17 / 112 (15%) |
| Smoky | 87 / 112 (78%) |
| Wood_and_or_Plant | 8 / 112 (7.1%) |
| (Missing) | 17 |
| brthFuel | |
| Mix | 53 / 116 (46%) |
| Smokeles | 5 / 116 (4.3%) |
| Smoky | 47 / 116 (41%) |
| Wood | 11 / 116 (9.5%) |
| (Missing) | 13 |
| cumFuel | |
| Mix | 82 / 119 (69%) |
| Smoky | 37 / 119 (31%) |
| (Missing) | 10 |
| curStove | |
| Firepit_and_unventilated | 22 / 112 (20%) |
| Mix | 19 / 112 (17%) |
| Portable_stove | 20 / 112 (18%) |
| Ventilated | 51 / 112 (46%) |
| (Missing) | 17 |
| bap_air | 65 (87) |
| (Missing) | 5 |
| pm25_air | 197 (176) |
| ANY_air | 1,038 (1,792) |
| (Missing) | 41 |
| BPE_air | 71 (92) |
| (Missing) | 5 |
| BaA_air | 88 (145) |
| (Missing) | 5 |
| BbF_air | 106 (143) |
| (Missing) | 5 |
| BkF_air | 23 (32) |
| (Missing) | 5 |
| CHR_air | 83 (133) |
| (Missing) | 5 |
| DBA_air | 24 (36) |
| (Missing) | 5 |
| FLT_air | 60 (136) |
| (Missing) | 5 |
| FLU_air | 486 (680) |
| (Missing) | 41 |
| IPY_air | 43 (51) |
| (Missing) | 5 |
| NAP_air | 5,731 (8,737) |
| (Missing) | 41 |
| PHE_air | 730 (1,054) |
| (Missing) | 41 |
| PYR_air | 66 (139) |
| (Missing) | 5 |
| Benzanthracene_Chrysene_urine | 0.92 (3.17) |
| (Missing) | 2 |
| Naphthalene_urine | 224 (686) |
| Methylnaphthalene_2_urine | 46 (59) |
| (Missing) | 9 |
| Methylnaphthalene_1_urine | 20 (24) |
| (Missing) | 4 |
| Acenaphthene_urine | 7 (11) |
| Phenanthrene_Anthracene_urine | 204 (275) |
| Fluoranthene_urine | 21 (23) |
| Pyrene_urine | 0.71 (0.57) |
| (Missing) | 18 |
| CUR6_BC_PAH6 | 0.21 (0.98) |
| (Missing) | 13 |
| CUR6_PAH31 | 0.20 (0.92) |
| (Missing) | 13 |
| CUR6_NkF | -0.11 (1.10) |
| (Missing) | 13 |
| CUR6_PM_RET | -0.01 (0.93) |
| (Missing) | 13 |
| CUR6_NO2 | 0.19 (0.99) |
| (Missing) | 13 |
| CUR6_SO2 | -0.13 (0.89) |
| (Missing) | 13 |
| CHLD5_X7 | -0.02 (0.92) |
| (Missing) | 13 |
| CHLD5_X33 | 0.18 (0.98) |
| (Missing) | 13 |
| CHLD5_NkF | -0.11 (1.13) |
| (Missing) | 13 |
| CHLD5_NO2 | 0.23 (1.09) |
| (Missing) | 13 |
| CHLD5_SO2 | 0.02 (0.88) |
| (Missing) | 13 |
| CUM6_BC_NO2_PM | 0.11 (1.01) |
| (Missing) | 13 |
| CUM6_PAH36 | 0.21 (0.97) |
| (Missing) | 13 |
| CUM6_DlP | -0.20 (1.04) |
| (Missing) | 13 |
| CUM6_NkF | -0.04 (1.11) |
| (Missing) | 13 |
| CUM6_RET | -0.09 (0.97) |
| (Missing) | 13 |
| CUM6_SO2 | -0.07 (0.93) |
| (Missing) | 13 |
| MEAS6_BC_PM_RET | 0.04 (0.93) |
| (Missing) | 85 |
| MEAS6_X31 | 0.06 (1.05) |
| (Missing) | 85 |
| MEAS6_X5 | 0.01 (1.00) |
| (Missing) | 85 |
| MEAS6_DlP | 0.02 (1.00) |
| (Missing) | 85 |
| MEAS6_NkF | 0.08 (1.04) |
| (Missing) | 85 |
| MEAS6_NO2_SO2 | -0.03 (0.99) |
| (Missing) | 85 |
| URI5_NAP_1M_2M | 0.01 (0.96) |
| (Missing) | 25 |
| URI5_ACE | -0.06 (0.99) |
| (Missing) | 25 |
| URI5_FLU_PHE | -0.05 (0.95) |
| (Missing) | 25 |
| URI5_PYR | -0.02 (0.91) |
| (Missing) | 25 |
| URI5_CHR | -0.01 (1.01) |
| (Missing) | 25 |
|
1
Mean (SD); n / N (%)
|
|
For observations in the control group
| Characteristic | N = 121 |
|---|---|
| SbjctD | NA (NA) |
| (Missing) | 12 |
| Visit | NA (NA) |
| (Missing) | 12 |
| Group | |
| LCW Clean Ctrl | 12 / 12 (100%) |
| Gender | |
| F | 12 / 12 (100%) |
| DNAmAge | 46 (14) |
| DNAmAgeHannum | 55 (10) |
| DNAmPhenoAge | 53 (10) |
| DNAmAgeSkinBloodClock | 48 (12) |
| DNAmGrimAge | 54 (8) |
| DNAmTL | 6.66 (0.44) |
| AgeAccelerationResidual | -5 (7) |
| AgeAccelerationResidualHannum | 2 (10) |
| AgeAccelPheno | 3 (10) |
| DNAmAgeSkinBloodClockAdjAge | -2.1 (5.9) |
| AgeAccelGrim | 3.6 (5.4) |
| DNAmTLAdjAge | -0.26 (0.51) |
| IEAA | -2.6 (6.1) |
| EEAA | 2 (12) |
| Age | 50 (11) |
| county | 0 / 0 (NA%) |
| (Missing) | 12 |
| BMI | NA (NA) |
| (Missing) | 12 |
| ses | NA (NA) |
| (Missing) | 12 |
| edu | NA (NA) |
| (Missing) | 12 |
| curFuel | |
| Gas/Elect | 12 / 12 (100%) |
| brthFuel | |
| Gas/Elect | 12 / 12 (100%) |
| cumFuel | |
| Gas/Elect | 12 / 12 (100%) |
| curStove | |
| Gas/Elect | 12 / 12 (100%) |
| bap_air | NA (NA) |
| (Missing) | 12 |
| pm25_air | NA (NA) |
| (Missing) | 12 |
| ANY_air | NA (NA) |
| (Missing) | 12 |
| BPE_air | NA (NA) |
| (Missing) | 12 |
| BaA_air | NA (NA) |
| (Missing) | 12 |
| BbF_air | NA (NA) |
| (Missing) | 12 |
| BkF_air | NA (NA) |
| (Missing) | 12 |
| CHR_air | NA (NA) |
| (Missing) | 12 |
| DBA_air | NA (NA) |
| (Missing) | 12 |
| FLT_air | NA (NA) |
| (Missing) | 12 |
| FLU_air | NA (NA) |
| (Missing) | 12 |
| IPY_air | NA (NA) |
| (Missing) | 12 |
| NAP_air | NA (NA) |
| (Missing) | 12 |
| PHE_air | NA (NA) |
| (Missing) | 12 |
| PYR_air | NA (NA) |
| (Missing) | 12 |
| Benzanthracene_Chrysene_urine | NA (NA) |
| (Missing) | 12 |
| Naphthalene_urine | NA (NA) |
| (Missing) | 12 |
| Methylnaphthalene_2_urine | NA (NA) |
| (Missing) | 12 |
| Methylnaphthalene_1_urine | NA (NA) |
| (Missing) | 12 |
| Acenaphthene_urine | NA (NA) |
| (Missing) | 12 |
| Phenanthrene_Anthracene_urine | NA (NA) |
| (Missing) | 12 |
| Fluoranthene_urine | NA (NA) |
| (Missing) | 12 |
| Pyrene_urine | NA (NA) |
| (Missing) | 12 |
| CUR6_BC_PAH6 | NA (NA) |
| (Missing) | 12 |
| CUR6_PAH31 | NA (NA) |
| (Missing) | 12 |
| CUR6_NkF | NA (NA) |
| (Missing) | 12 |
| CUR6_PM_RET | NA (NA) |
| (Missing) | 12 |
| CUR6_NO2 | NA (NA) |
| (Missing) | 12 |
| CUR6_SO2 | NA (NA) |
| (Missing) | 12 |
| CHLD5_X7 | NA (NA) |
| (Missing) | 12 |
| CHLD5_X33 | NA (NA) |
| (Missing) | 12 |
| CHLD5_NkF | NA (NA) |
| (Missing) | 12 |
| CHLD5_NO2 | NA (NA) |
| (Missing) | 12 |
| CHLD5_SO2 | NA (NA) |
| (Missing) | 12 |
| CUM6_BC_NO2_PM | NA (NA) |
| (Missing) | 12 |
| CUM6_PAH36 | NA (NA) |
| (Missing) | 12 |
| CUM6_DlP | NA (NA) |
| (Missing) | 12 |
| CUM6_NkF | NA (NA) |
| (Missing) | 12 |
| CUM6_RET | NA (NA) |
| (Missing) | 12 |
| CUM6_SO2 | NA (NA) |
| (Missing) | 12 |
| MEAS6_BC_PM_RET | NA (NA) |
| (Missing) | 12 |
| MEAS6_X31 | NA (NA) |
| (Missing) | 12 |
| MEAS6_X5 | NA (NA) |
| (Missing) | 12 |
| MEAS6_DlP | NA (NA) |
| (Missing) | 12 |
| MEAS6_NkF | NA (NA) |
| (Missing) | 12 |
| MEAS6_NO2_SO2 | NA (NA) |
| (Missing) | 12 |
| URI5_NAP_1M_2M | NA (NA) |
| (Missing) | 12 |
| URI5_ACE | NA (NA) |
| (Missing) | 12 |
| URI5_FLU_PHE | NA (NA) |
| (Missing) | 12 |
| URI5_PYR | NA (NA) |
| (Missing) | 12 |
| URI5_CHR | NA (NA) |
| (Missing) | 12 |
|
1
Mean (SD); n / N (%)
|
|
Fuel Types Summary table
Current Fuel vs Birth Fuel + Cumulative
## brthFuel cumFuel Gas/Elect Smokeles Smoky Wood_and_or_Plant NA
## 1 Gas/Elect Gas/Elect 12 0 0 0 0
## 2 Mix Mix 0 9 36 6 2
## 3 Smokeles Mix 0 2 3 0 0
## 4 Smoky Mix 0 3 7 0 0
## 5 Smoky Smoky 0 0 35 0 2
## 6 Wood Mix 0 2 4 2 3
## 7 <NA> Mix 0 1 2 0 0
## 8 <NA> <NA> 0 0 0 0 10PCA
Only the treatment group are used in this PCA exploration. 
Explore clocks
Clock values
Correlogram
Between clocks
{r correlation_clocks, fig.height=6, fig.width=6} # library(corrplot) # corrplot(cor(df[,c("Age", clocks_vars)]), addCoef.col = 'black', type = 'lower') #
All subjects
Control Group
Treatment Group
Median absolute error
## DNAmAge DNAmAgeHannum DNAmPhenoAge
## 3.645646 3.595255 3.061584
## DNAmAgeSkinBloodClock DNAmGrimAge
## 2.585191 3.993800Scatterplots of age vs each epigenetic age
All subjects
Control Group
Treatment Group
Explore Exposure Measurements
Correlogram
Between Ambient Exposure Measurements
Between Urinary Exposure Measurements
Between Ambient and Urinary Exposure Measurements
Clocks vs Measurements
Pairplots
